Structure of proline utilization a with the FAD covalently modified by tetrahydrothiophene

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 15% strand (DSSP).

Ligands and binding sites

• UJG · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-{7, 8-dimethyl-2,4-dioxo-5-[(2R)-tetrahydrothiophen-2-yl]-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl}-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) · ligand · 2 copies · chains A, B
• NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal
• SO4 · Sulfate ion · ion · 6 copies · chains A, B
• FMT · Formic acid · additive · 5 copies · chains A, B
• PGE · Triethylene glycol · additive · 3 copies · chains A, B
• PEG · Di(hydroxyethyl)ether · additive · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1944 Ų buried · 36 hydrogen bonds · protein-protein

Compared structures

• 7MYC · Structure of proline utilization A with the FAD covalently modified by tetrahydrothiophene · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt F7X6I3
• Elsewhere: RCSB PDB 7MYC · PDBe 7MYC · UniProt F7X6I3